BamQC report ----------------------------------- >>>>>>> Input bam file = SRR9716765.sorted.bam outfile = /home/luna/rawdata/yangyxdownload/SRP215441/SRP215441.result/quality.files/genome_results.txt >>>>>>> Reference number of bases = 3,095,693,983 bp number of contigs = 25 >>>>>>> Globals number of windows = 424 number of reads = 746,973 number of mapped reads = 685,686 (91.8%) number of supplementary alignments = 2,894 (0.39%) number of secondary alignments = 0 number of mapped bases = 39,829,779 bp number of sequenced bases = 39,818,034 bp number of aligned bases = 0 bp number of duplicated reads (estimated) = 20,442 duplication rate = 2.23% >>>>>>> Insert size mean insert size = 0 std insert size = 0 median insert size = 0 >>>>>>> Mapping quality mean mapping quality = 44.842 >>>>>>> ACTG content number of A's = 9,710,232 bp (24.39%) number of C's = 7,464,243 bp (18.75%) number of T's = 12,827,457 bp (32.22%) number of G's = 9,815,275 bp (24.65%) number of N's = 827 bp (0%) GC percentage = 43.4% >>>>>>> Mismatches and indels general error rate = 0.0052 number of mismatches = 199,525 number of insertions = 2,866 mapped reads with insertion percentage = 0.42% number of deletions = 7,333 mapped reads with deletion percentage = 1.06% homopolymer indels = 41.73% >>>>>>> Coverage mean coverageData = 0.0129X std coverageData = 0.1511X There is a 1.2% of reference with a coverageData >= 1X There is a 0.06% of reference with a coverageData >= 2X There is a 0.01% of reference with a coverageData >= 3X There is a 0% of reference with a coverageData >= 4X There is a 0% of reference with a coverageData >= 5X There is a 0% of reference with a coverageData >= 6X There is a 0% of reference with a coverageData >= 7X There is a 0% of reference with a coverageData >= 8X There is a 0% of reference with a coverageData >= 9X There is a 0% of reference with a coverageData >= 10X There is a 0% of reference with a coverageData >= 11X There is a 0% of reference with a coverageData >= 12X There is a 0% of reference with a coverageData >= 13X There is a 0% of reference with a coverageData >= 14X There is a 0% of reference with a coverageData >= 15X There is a 0% of reference with a coverageData >= 16X There is a 0% of reference with a coverageData >= 17X There is a 0% of reference with a coverageData >= 18X There is a 0% of reference with a coverageData >= 19X There is a 0% of reference with a coverageData >= 20X There is a 0% of reference with a coverageData >= 21X There is a 0% of reference with a coverageData >= 22X There is a 0% of reference with a coverageData >= 23X There is a 0% of reference with a coverageData >= 24X There is a 0% of reference with a coverageData >= 25X There is a 0% of reference with a coverageData >= 26X There is a 0% of reference with a coverageData >= 27X There is a 0% of reference with a coverageData >= 28X There is a 0% of reference with a coverageData >= 29X There is a 0% of reference with a coverageData >= 30X There is a 0% of reference with a coverageData >= 31X There is a 0% of reference with a coverageData >= 32X There is a 0% of reference with a coverageData >= 33X There is a 0% of reference with a coverageData >= 34X There is a 0% of reference with a coverageData >= 35X There is a 0% of reference with a coverageData >= 36X There is a 0% of reference with a coverageData >= 37X There is a 0% of reference with a coverageData >= 38X There is a 0% of reference with a coverageData >= 39X There is a 0% of reference with a coverageData >= 40X There is a 0% of reference with a coverageData >= 41X There is a 0% of reference with a coverageData >= 42X There is a 0% of reference with a coverageData >= 43X There is a 0% of reference with a coverageData >= 44X There is a 0% of reference with a coverageData >= 45X There is a 0% of reference with a coverageData >= 46X There is a 0% of reference with a coverageData >= 47X There is a 0% of reference with a coverageData >= 48X There is a 0% of reference with a coverageData >= 49X There is a 0% of reference with a coverageData >= 50X There is a 0% of reference with a coverageData >= 51X >>>>>>> Coverage per contig chr1 249250621 3231595 0.012965243524909813 0.21234837890778685 chr2 243199373 3331112 0.013697041891633495 0.21532341323329227 chr3 198022430 2625109 0.013256624514707754 0.12157551365268125 chr4 191154276 2547646 0.013327695583435445 0.13716747353686592 chr5 180915260 2383361 0.013173908049547618 0.12095932937229988 chr6 171115067 2225983 0.013008690812714932 0.1271713104396576 chr7 159138663 2188367 0.01375132201531692 0.1644878111595424 chr8 146364022 1995246 0.013632079610384033 0.17284955498950094 chr9 141213431 1674576 0.011858475416548728 0.13210415139555765 chr10 135534747 1961112 0.014469440814317527 0.16714821298135513 chr11 135006516 1796048 0.013303417147658265 0.1330807747273499 chr12 133851895 1792722 0.013393325511006027 0.12299380123527293 chr13 115169878 1211706 0.010521032244212327 0.1084799466428964 chr14 107349540 1203277 0.011208962795741835 0.11317215512191517 chr15 102531392 1168315 0.011394705340584862 0.11215179553990348 chr16 90354753 1186021 0.013126271287576869 0.12479023055962159 chr17 81195210 1132488 0.013947719329748639 0.12839841555418455 chr18 78077248 1042876 0.013356976926235924 0.17819237149937875 chr19 59128983 852759 0.014422013651071928 0.16572079168734583 chr20 63025520 867760 0.013768390962898839 0.12611127550591567 chr21 48129895 529126 0.010993707756894129 0.1293836846374532 chr22 51304566 494050 0.009629747184685277 0.10376992200868895 chrMT 16571 12206 0.7365880152072899 0.9805053718795133 chrX 155270560 2216285 0.014273697473622816 0.1308690997860872 chrY 59373566 160033 0.002695357728723924 0.1290215169669598